France accepted the Ocean Viking and the 234 migrants onboard, but in return said it would suspend a previous plan to take in 3,500 refugees currently in Italy, and urged other EU nations to do the same.
"I was very struck by the aggressive reaction of the French government, which is incomprehensible and unjustified," Meloni told a press conference in Rome.
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The ship docked at the French port of Toulon on Friday morning, as relations between the two countries soured further.
The Ocean Viking, operated by a French NGO, had picked up the migrants at sea near the Libyan coast before spending weeks seeking a port to accept them.
France had never before allowed a rescue vessel carrying migrants from the Mediterranean to land on its coast, but did so this time because Italy had refused access.
French Interior Minister Gerald Darmanin said on Thursday that the migrants were Italy's responsibility under EU rules, and that the French move was an "exceptional" measure.
He said Italy's refusal to accept the migrants was "incomprehensible" and that there would be "severe consequences" for Italy's bilateral relations with France, and with the European Union as a whole.
He said France had acted according to its "humanitarian duty", while Italy had "lacked humanity".
The Ocean Viking ship had initially sought access to Italy's coast, which is closest to where the migrants were picked up, saying health and sanitary conditions onboard were rapidly worsening.
Italy refused, saying other nations needed to take in more of the migrants trying to reach Europe from North Africa every year.
The migrants, more than 50 of whom are children, were taken to an “international waiting zone” pending the processing of requests for asylum.
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They would not be allowed to leave the zone until the process was completed in about three weeks, the government said. Asylum interviews were to start on Saturday.
The shelter, a short drive from the port, was heavily guarded, an AFP photographer said.
Some 600 police were deployed for the ship's arrival, with the Red Cross in charge of humanitarian aid.
Nine European nations have committed to hosting two-thirds of the migrants, Darmanin said Thursday, with the remaining third staying in France.
Germany will take "more than 80", while Croatia, Romania, Bulgaria, Lithuania, Malta, Portugal, Luxembourg and Ireland will also contribute in the name of "European solidarity", he said.
So far this year, 164 asylum seekers have been moved from Italy to other nations in the bloc that volunteered to accept them.
That is a fraction of the more than 88,000 that have reached its shores so far this year, of which 14 percent arrived after being rescued by NGO vessels, according to Italian authorities.
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